Dear libmesh developers
VTK output crashes when run in parallel (mpirun -n 2 ...). The following
assertion fails:
Assertion `it!=_global_to_local_map.end()' failed.
[...]/libmesh/include/numerics/petsc_vector.h, line 1073, [...]
The problem is reproducible with the following minimal working example:
//START MINIMAL WORKING EXAMPLE CODE
#include "libmesh.h"
#include "mesh.h"
#include "mesh_generation.h"
#include "equation_systems.h"
#include "explicit_system.h"
#include "vtk_io.h"
using namespace libMesh;
int main(int argc, char** argv)
{
LibMeshInit init(argc, argv);
{
Mesh mesh;
MeshTools::Generation::build_line(mesh, 4, 0, 1, EDGE2);
EquationSystems equation_systems(mesh);
ExplicitSystem& system = equation_systems.add_system<ExplicitSystem>("sys");
system.add_variable("u");
equation_systems.init();
VTKIO(mesh).write_equation_systems("out.pvtu", equation_systems); // causes
assertion failure
}
return 0;
}
//END MINIMAL WORKING EXAMPLE CODE
The stack trace looks as follows:
0: libMesh::print_trace(std::ostream&)
1: libMesh::PetscVector<double>::map_global_to_local_index(unsigned int) const
2: libMesh::PetscVector<double>::operator()(unsigned int) const
3: libMesh::System::current_solution(unsigned int) const
4: libMesh::VTKIO::solution_to_vtk(libMesh::EquationSystems const&,
vtkUnstructuredGrid*&)
5: libMesh::VTKIO::write_equation_systems(std::string const&,
libMesh::EquationSystems const&)
6: main
7: __libc_start_main
The assertion does NOT fail when running in serial mode (without mpirun) or
when using ExodusII_IO. Since I'm bound to VTK and parallel processing, I will
need to fix this. The problem seems to be that current_solution.operator() is
called for ALL dofs in line 333 of vtk_io.C, instead of only the local ones.
Therefore, the global-to-local index map doesn't contain the sought indices,
when processor 0 attempts to write data owned by processor 1.
Solution output appears to be more sophisticated in ExodusII_IO, where
MeshOutput<MT>::_build_variable_names_and_solution_vector is called, which does
a EquationSystems::allgather().
What's the expert's ansatz to fixing VTK output? Should I have a go at
duplicating the ExodusII output procedure, or does anybody see a simple(r) way
of fixing the problem? Perhaps a localize_to_one() call on the solution vector?
Would that compromise parallel efficiency?
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